title: ChIP H3K4 dimethyl Treg replicate 3


title: ChIP H3K4 trimethyl Treg replicate 2

status: Public on May 11 2009

type: genomic

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Rengensburg Center for Interventional Immunology

hyb_protocol: Samples were hybridized using a stringent protocol.The differentially labeled input and ChIP sample were combined and supplemented with 25 µg human Cot-1 DNA (Invitrogen), 26 µl of Agilent blocking agent (10-fold) (Agilent) and 130 µl Agilent hybridization buffer (2-fold) as supplied in the Agilent oligo aCGH Hybridization kit. The samples were heated to 95° for 3 min, mixed and subsequently incubated at 37°C for 30 min. Hybridization was then carried out 65°C for 40 h using an SureHyb chamber and an Agilent hybridization oven. Slides were washed in Wash I (6xSSPE, 0.005% N-lauroylsarcosine) at room temperature for 5 min and in Wash II (0.06xSSPE) for an additional 5 min. Afterwards slides were dried using acetonitrile within an ozone free facility.

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution.Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used. Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis. Probes with abnormal hybridization behavior (extremely low (2507 probes) or high (5149 probes) signal intensities in both channels) were excluded.

label: Alexa Fluor 555–aha–dCTP

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4+CD25+CD45RA+ Treg

label_protocol: ChIP samples were amplified with ligation mediated PCR (LM-PCR) prior to labeling: ChIP and input DNA were blunted and phosphorylated for 30 minutes at 20 °C in 50 µl reactions containing 10x T4 DNA ligase buffer, 2 µl dNTP mix (10 mM each), 3 U T4 DNA polymerase, 10 U T4 polynucleotide kinase and 1 U Klenow DNA polymerase. Purification using the Qiaquick PCR purification kit (Qiagen) was followed by the addition of Adenine to 3’-ends using Klenow fragment (3’ to 5’ exo minus), and dATP (1 mM) for 30 minutes at 37 °C. After clean-up using the MinElute kit (Qiagen), DNA fragments were ligated to linker DNA (60 µM pre-annealed JW102s 5'-GCG GTG ACC CGG GAG ATC TGA ATT CT-3' and JW103 5'-GAA TTC AGA TC-3') with 4 µl DNA Quick-Ligase (NEB) in a 30 µl reaction for 15 minutes at RT. Samples were cleaned-up (Qiaquick PCR purification kit (Qiagen)) and amplified using Phusion Polymerase and JW102s oligonucleotide for 15 cycles. The product of the first amplification was diluted 1/20 with ddH2O and 5 µl of the dilution were used for a second round of amplification (15 cycles) using Phusion Polymerase HOT START and JW102s oligonucleotide. The amplified ChIP and input material was purified using Qiaquick PCR purification kit (Qiagen). Then 1µg each of the samples were fluorescently labeled for microarray hybridization by direct labeling with Alexa Fluor 555–aha–dCTP and Alexa Fluor 647–aha–dCTP using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen; Version A, 12 February 2007) according to the manufacturer's intruction.

growth_protocol: Treg and Tconv cell isolation and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).

extract_protocol: Genomic DNA was prepared using the Qiagen Blood & Cell Culture DNA Kit or the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instruction.

treatment_protocol: Treg and Tconv cell FACS sorting and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).

tag: Antibody from Upstate

tag: gender

value: male

tag: CD4+CD25+CD45RA+ regulatory T-cells

tag: expansion cultures

label: Alexa Fluor 647–aha–dCTP

source_name: Input (4% volumen of Lysate)


title: ChIP H3K4 monomethyl Tconv replicate 3

source_name: CD4+CD25- Tconv

tag: Antibody from Abcam

tag: CD4+CD25- conventional T-cells


title: ChIP H3K4 trimethyl Treg replicate 1


title: ChIP CTCF Tconv replicate 1

tag: Antibody is a gift from V. Lobanenkow


title: ChIP H3K4 dimethyl Tconv replicate 3


title: ChIP H3K4 monomethyl Tconv replicate 2


title: ChIP H3K4 dimethyl Tconv replicate 2


title: ChIP H3K4 trimethyl Tconv replicate 2


title: ChIP H3K4 dimethyl Treg replicate 2


title: ChIP H3K4 monomethyl Treg replicate 2


title: ChIP H3K4 monomethyl Tconv replicate1


title: ChIP H3K4 trimethyl Tconv replicate 1


title: ChIP H3K4 dimethyl Treg replicate 1


title: Treg and Tconv cells hypomethylated pools Replicate 2

description: Biological replicate 2 of 2; samples hypo-rep2 and hyper-rep2 originate from the same gDNA preparation that was separated into an unmethylated and a methylated fraction by MCIp

hyb_protocol: Samples were hybridized using a stringent protocol.The differentially labeled genomic pools (ether hypo or hyper) were combined (Treg hypo with Tconv hypo or Treg hyper with Tconv Hyper respectively) and supplemented with 25 µg human Cot-1 DNA (Invitrogen), 26 µl of Agilent blocking agent (10-fold) (Agilent) and 130 µl Agilent hybridization buffer (2-fold) as supplied in the Agilent oligo aCGH Hybridization kit. The samples were heated to 95° for 3 min, mixed and subsequently incubated at 37°C for 30 min. Hybridization was then carried out 65°C for 40 h using an SureHyb chamber and an Agilent hybridization oven. Slides were washed in Wash I (6xSSPE, 0.005% N-lauroylsarcosine) at room temperature for 5 min and in Wash II (0.06xSSPE) for an additional 5 min. Afterwards slides were dried using acetonitrile within an ozone free facility.

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

source_name: CD4+CD25+CD45RA+ Treg from expansion cultures, hypomethylated pool (hypo) culture 2

label_protocol: MCIp treated genomic DNA pools were fluorescently labeled for microarray hybridization by direct labeling with Alexa Fluor 555–aha–dCTP and Alexa Fluor 647–aha–dCTP using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen; Version A, 12 February 2007) according to the manufacturer's intruction.

tag: Age

value: d11  expansion cultures

source_name: CD4+CD25- Tconv from expansion cultures, hypomethylated pool (hypo) culture 2


title: ChIP H3K4 monomethyl Treg replicate 3


title: Treg and Tconv cells hypermethylated pools Replicate 2

source_name: CD4+CD25+CD45RA+ Treg from expansion cultures, hypermethylated pool (hypo) culture 2

source_name: CD4+CD25- Tconv from expansion cultures, hypermethylated pool (hypo) culture 2


title: Treg and Tconv cells hypermethylated pools Replicate 1

description: Biological replicate 1 of 2; samples hypo-rep1 and hyper-rep1 originate from the same gDNA preparation that was separated into an unmethylated and a methylated fraction by MCIp

source_name: CD4+CD25+CD45RA+ Treg from expansion cultures, hypermethylated pool (hypo) culture 1

source_name: CD4+CD25- Tconv from expansion cultures, hypermethylated pool (hypo) culture 1


title: ChIP H3K4 monomethyl Treg replicate 1


title: L3Trachea_NP2610::UAS-PGRP-LE_technicalreplicate2

type: RNA

city: Kiel

first: Christina

last: Wagner

address: Am Botanischen Garten 1-9

department: Zoophysiology

institute: Zoological Institute

description: nothing left

hyb_protocol: No blocking: Hybridisation of labeled cRNA in DigEasy hyb (Roche) overnight at 42°C in hyb chambers. Washing: 2x15 min 1xSSC and 0.1% Triton-X-100 at 60°C 2x15 min 0.1xSSC and 0.1% Triton-X-100 at 37°C 1x30 sec 0.1xSSC 1x10 sec water

scan_protocol: digitalisation of the fluorescence intensities was carried out using the GenePix 4000B scanner. scanner release: 10 µm laser power: 100%

data_processing: for spot finding and generating preliminary result files the raw scanned image files were analysed using the GenePixPro version 6.0 whereas data normalisation (sub-grid), quality assurance and control, filtering and clustering were carried out with GeneTraffic (Iobion).

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: Two-step method used to generate labeled aacRNA. In the first step amino-allyl UTPs are incorporated during cRNA synthesis. Subsequently, monofunctional forms of Cy3 dyes are reacted with the amino-allyl cRNA

growth_protocol: F1-generation of the cross was raised on a standard cornmeal-yeast agar medium at 22°C till the larvae have reached their third instar larva stage (approximately 10 days).

extract_protocol:
RNA was extracted from 20 pairs of trachea using the manufacture protocoll of Macharay and Nagel, NucleoSpin Kit II.
cDNA was synthesised from RNA using Superscript III-Kit from Invitrogen and amplified by the CapFinder strategy.
cRNA was synthesised from the amplified DNA using the Ambion's MEGAscript High Yield Transcription Kit.

treatment_protocol: Overexpression of the pattern recognition receptor PGRP-LE in the larval trachea using the binary GAL/UAS-system of Brand and Perrimon. The driver strain (NP2610) is derived from DGRC (Drosophila Genetic Resource Center) and the UAS-effector strain was provided us from the Kurata lab (Kurata et al., 2002).

tag: Strain:F1-generation of the following cross

tag: Stage

value: third instar larva

value: 10 days

tag: Tissue

value: Trachea

label_protocol: Two-step method used to generate labeled aacRNA. In the first step amino-allyl UTPs are incorporated during cRNA synthesis. Subsequently, monofunctional forms of Cy5 dyes are reacted with the amino-allyl cRNA.

growth_protocol: Larvae were raised on a standard cornmeal-yeast agar medium at 22°C till the larvae have reached their third instar larva stage (approximately 10 days).

treatment_protocol: Trachea of third instar larvae of the driver strain was used as control

tag: Strain


title: ChIP H3K4 trimethyl Tconv replicate 3


title: L3Trachea_NP2610::UAS-PGRP-LE_biologicalreplicate2

description: nothing left


title: wSan v wMel mCGH sample 1

city: Baltimore

first: Julie

middle: C

last: Dunning Hotopp

state: MD

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

country: USA

institute: Univeristy of Maryland Baltimore

description: Cy3- and Cy5-labeled probes were synthesized from a pool of three distinct GenomiPhi amplifications to reduce bias. One flip-dye experiment (two hybridizations) was performed with each of three independent pools, yielding a total of six hybridizations/strain. With 4-8 printed replicates per slide this yielded 24-48 replicated spots per gene to compare across the study. The geometric mean ratio was calculated for all good spots in each flip-dye experiment. The values reported in the manuscript and supplementary file are the medians of the geometric mean ratio for the three flip-dye experiments.

hyb_protocol: Probe pairs were resuspended in 5X SSC, 50% formamide, 0.1% SDS, 0.1 mM DTT, and 0.35 mg/mL salmon sperm DNA and hybridized to slides overnight at 42 oC. The hybridized slides were washed twice in 2X SSC, 0.1% SDS at 55 oC; twice in 0.1X SSC, 0.1% SDS at room temperature; twice in 0.1X SSC at room temperature; and once in MilliQ water at room temperature.

scan_protocol: Scanned using a GenePix4000B scanner (Molecular Devices).

data_processing: Ratios were normalized using iterative log mode centering.

organism: Wolbachia pipientis

source_name: Cy3 wSan (wSan v wMel mCGH sample 1)

label_protocol: Cy3 and Cy5 probes were synthesized from GenomiPhi amplified DNAs. Amino-allyl-dUTP labeled probes were synthesized from 4 μg of genomic DNA using Klenow Fragment (3' → 5' exo-) (New England Biolabs). The reactions were purified using QIAquick PCR purification kit (Qiagen) using modified phosphate buffers. Cy3- or Cy5-dyes (GE Healthcare) were chemically coupled to the incorporated amino-allyl dUTP in carbonate buffer.

extract_protocol: Wolbachia cells were isolated from 2-4 g live, whole insects via density centrifugation and whole chromosomal fragments were purified following pulsed field gel separation as previously described.  Due to the small amounts of chromosomal fragments recovered, whole genome amplification was needed to produce enough DNA for hybridization.  Therefore ~10 ng of genomic DNA was amplified per reaction with GenomiPhi. To reduce the effects of any bias, each probe was synthesized from a pool of three distinct GenomiPhi amplifications.

value: wSan

source_name: Cy5 wMel (wSan v wMel mCGH sample 1)

value: wMel


title: L3Trachea_NP2610::UAS-PGRP-LE_technicalreplicate1

description: nothing left


title: wSan v wMel mCGH sample 3

source_name: Cy3 wSan (wSan v wMel mCGH sample 3)

source_name: Cy5 wMel (wSan v wMel mCGH sample 3)


title: L3Trachea_NP2610::UAS-PGRP-LE_biologicalreplicate1

description: nothing left

hyb_protocol: No blocking: Hybridisation of labeled cRNA in DigEasy hyb (Roche) overnight at 42°C in hyb chambers. Washing: 2x15 min 1xSSC and 0.1% Triton-X-100 at 60°C              2x15 min 0.1xSSC and 0.1% Triton-X-100 at 37°C              1x30 sec 0.1xSSC              1x10 sec water

scan_protocol: digitalisation of the fluorescence intensities was carried out using the  GenePix 4000B scanner. scanner release: 10 µm laser power: 100%

label_protocol: Two-step method used to generate labeled aacRNA. In the first step amino-allyl UTPs are incorporated during cRNA synthesis. Subsequently, monofunctional forms of Cy3 dyes are reacted with the amino-allyl cRNA.


title: human non-Hodgkins lymphoma cell line, U-698-M_rep2

city: South San Francisco

first: Peng

last: Yue

state: CA

address: 1 DNA Way

institute: Genentech Inc

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Expression was normalized and estimated using the GC-RMA package of BioConductor.

label: biotin

source_name: human non-Hodgkins lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in RPMI1640 or DMEM supplemented with 10% fetal bovine serum, non-essential amino acids and 2mmol/L L-glutamine.

extract_protocol: Qiagen Rneasy kit used for the extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were untreated.

tag: cell line

tag: cell type

value: human non-Hodgkins lymphoma


title: Treg and Tconv cells hypomethylated pools Replicate 1

source_name: CD4+CD25+CD45RA+ Treg from expansion cultures, hypomethylated pool (hypo) culture 1

source_name: CD4+CD25- Tconv from expansion cultures, hypomethylated pool (hypo) culture 1


title: wMel v wSan mCGH sample 2

source_name: Cy3 wMel (wMel v wSan mCGH sample 2)

source_name: Cy5 wSan (wMel v wSan mCGH sample 2)


title: wMel v wSan mCGH sample 1

source_name: Cy3 wMel (wMel v wSan mCGH sample 1)

source_name: Cy5 wSan (wMel v wSan mCGH sample 1)


title: human non-Hodgkins lymphoma cell line, U-698-M_rep1


title: wSim v wMel mCGH sample 2

source_name: Cy3 wSim (wSim v wMel mCGH sample 2)

value: wSim

source_name: Cy5 wMel (wSim v wMel mCGH sample 2)


title: human non-Hodgkins lymphoma cell line, WSU-NHL

description: WSU-NHL

value: WSU-NHL


title: wSan v wMel mCGH sample 2

source_name: Cy3 wSan (wSan v wMel mCGH sample 2)

source_name: Cy5 wMel (wSan v wMel mCGH sample 2)


title: wSim v wMel mCGH sample 3

source_name: Cy3 wSim (wSim v wMel mCGH sample 3)

source_name: Cy5 wMel (wSim v wMel mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, WSU-FSCCL_rep2

value: WSU-FSCCL


title: human non-Hodgkins lymphoma cell line, WSU-DLCL2


title: human non-Hodgkins lymphoma cell line, WSU-FSCCL_rep1


title: wMel v wSim mCGH sample 3

source_name: Cy3 wMel (wMel v wSim mCGH sample 3)

source_name: Cy5 wSim (wMel v wSim mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, TK_rep2

value: TK


title: wSim v wMel mCGH sample 1

source_name: Cy3 wSim (wSim v wMel mCGH sample 1)

source_name: Cy5 wMel (wSim v wMel mCGH sample 1)


title: human non-Hodgkins lymphoma cell line, SU-DHL-5

source_name: human non-Hodgkins lymphoma cell line


title: human non-Hodgkins lymphoma cell line, SU-DHL-6


title: wInn v wMel mCGH sample 2

source_name: Cy3 wInn (wInn v wMel mCGH sample 2)

value: wInn

source_name: Cy5 wMel (wInn v wMel mCGH sample 2)


title: wMel v wInn mCGH sample 3

source_name: Cy3 wMel (wMel v wInn mCGH sample 3)

source_name: Cy5 wInn (wMel v wInn mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, SU-DHL-8_rep2


title: wMel v wInn mCGH sample 2

source_name: Cy3 wMel (wMel v wInn mCGH sample 2)

source_name: Cy5 wInn (wMel v wInn mCGH sample 2)


title: human non-Hodgkins lymphoma cell line, SU-DHL-4_rep5


title: human non-Hodgkins lymphoma cell line, Sc-1


title: wMel v wSim mCGH sample 2

source_name: Cy3 wMel (wMel v wSim mCGH sample 2)

source_name: Cy5 wSim (wMel v wSim mCGH sample 2)


title: wInn v wMel mCGH sample 3

source_name: Cy3 wInn (wInn v wMel mCGH sample 3)

source_name: Cy5 wMel (wInn v wMel mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, TK_rep1


title: wInn v wMel mCGH sample 1

source_name: Cy3 wInn (wInn v wMel mCGH sample 1)

source_name: Cy5 wMel (wInn v wMel mCGH sample 1)


title: wMel v wSim mCGH sample 1

source_name: Cy3 wMel (wMel v wSim mCGH sample 1)

source_name: Cy5 wSim (wMel v wSim mCGH sample 1)


title: wRi v wMel mCGH sample 2

source_name: Cy3 wRi (wRi v wMel mCGH sample 2)

value: wRi

source_name: Cy5 wMel (wRi v wMel mCGH sample 2)


title: wRi v wMel mCGH sample 3

source_name: Cy3 wRi (wRi v wMel mCGH sample 3)

source_name: Cy5 wMel (wRi v wMel mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, Toledo

description: Toledo

source_name: human non-Hodgkins lymphoma cell line

value: Toledo


title: wMel v wSan mCGH sample 3

source_name: Cy3 wMel (wMel v wSan mCGH sample 3)

source_name: Cy5 wSan (wMel v wSan mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, SU-DHL-4_rep2


title: human non-Hodgkins lymphoma cell line, SU-DHL-8_rep1


title: human non-Hodgkins lymphoma cell line, SU-DHL-4_rep4


title: wAu v wMel mCGH sample 1

source_name: Cy3 wAu (wAu v wMel mCGH sample 1)

value: wAu

source_name: Cy5 wMel (wAu v wMel mCGH sample 1)


title: wMel v wInn mCGH sample 1

source_name: Cy3 wMel (wMel v wInn mCGH sample 1)

source_name: Cy5 wInn (wMel v wInn mCGH sample 1)


title: wRi v wMel mCGH sample 1

source_name: Cy3 wRi (wRi v wMel mCGH sample 1)

source_name: Cy5 wMel (wRi v wMel mCGH sample 1)


title: human non-Hodgkins lymphoma cell line, SU-DHL-4_rep1


title: human non-Hodgkins lymphoma cell line, SU-DHL-1_rep2


title: wMel v wAu mCGH sample 1

source_name: Cy3 wMel (wMel v wAu mCGH sample 1)

source_name: Cy5 wAu (wMel v wAu mCGH sample 1)


title: wMel v wRi mCGH sample 3

source_name: Cy3 wMel (wMel v wRi mCGH sample 3)

source_name: Cy5 wRi (wMel v wRi mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, SU-DHL-4_rep3


title: wMel v wRi mCGH sample 2

source_name: Cy3 wMel (wMel v wRi mCGH sample 2)

source_name: Cy5 wRi (wMel v wRi mCGH sample 2)


title: wAu v wMel mCGH sample 3

source_name: Cy3 wAu (wAu v wMel mCGH sample 3)

source_name: Cy5 wMel (wAu v wMel mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, SCC-3_rep2

source_name: human non-Hodgkins lymphoma cell line


title: human non-Hodgkins lymphoma cell line, SU-DHL-1_rep1


title: human non-Hodgkins lymphoma cell line, SR

description: SR

value: SR


title: human non-Hodgkins lymphoma cell line, RI_1


title: human non-Hodgkins lymphoma cell line, SU-DHL-10_rep2


title: human non-Hodgkins lymphoma cell line, SCC-3_rep1


title: human non-Hodgkins lymphoma cell line, SU-DHL-16_rep1


title: wMel v wAu mCGH sample 3

source_name: Cy3 wMel (wMel v wAu mCGH sample 3)

source_name: Cy5 wAu (wMel v wAu mCGH sample 3)


title: human non-Hodgkins lymphoma cell line, RL_rep2

value: RL


title: human non-Hodgkins lymphoma cell line, SU-DHL-16_rep2


title: human non-Hodgkins lymphoma cell line, Ramos_rep1

value: Ramos


title: human non-Hodgkins lymphoma cell line, SU-DHL-10_rep1


title: wAu v wMel mCGH sample 2

source_name: Cy3 wAu (wAu v wMel mCGH sample 2)

source_name: Cy5 wMel (wAu v wMel mCGH sample 2)


title: human non-Hodgkins lymphoma cell line, RL_rep1


title: human non-Hodgkins lymphoma cell line, Ramos_rep2


title: human non-Hodgkins lymphoma cell line, RC-K8_rep1


title: wMel v wAu mCGH sample 2

source_name: Cy3 wMel (wMel v wAu mCGH sample 2)

source_name: Cy5 wAu (wMel v wAu mCGH sample 2)


title: wMel v wRi mCGH sample 1

source_name: Cy3 wMel (wMel v wRi mCGH sample 1)

source_name: Cy5 wRi (wMel v wRi mCGH sample 1)


title: human non-Hodgkins lymphoma cell line, REC-1


title: human non-Hodgkins lymphoma cell line, OCI-Ly19_rep2


title: Treg_freshly sorted_CD4+CD25+_rep1

description: gender: male

hyb_protocol: Samples were hybridized using a stringent protocol according to the manufacture's instruction. 1.65 µg labeled cRNA was supplemented with 11 µl Agilent 10x blocking agent, 2.2 µl Agilent 25x fragmentation buffer and nuclease-free water up to 55 µl final volumen. The sample was incubated at 60°C for 30 minutes, supplemented with 55 µl 2x hybridisation buffer and 100 µl of the mix was hybridisized for 16h at 65°C using an SureHyb chamber and an Agilent hybridization oven. Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE)  wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.

scan_protocol: Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.

data_processing: Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 7.

source_name: freshly sorted Treg cells

label_protocol: Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 200 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.

extract_protocol: Total cellular RNA of the different cell types was isolated using the RNeasy Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.

tag: Treg freshly sorted CD4+CD25+


title: human non-Hodgkins lymphoma cell line, RC-K8_rep2


title: human non-Hodgkins lymphoma cell line, Pfeiffer

description: Pfeiffer

value: Pfeiffer


title: Treg_freshly sorted_CD4+CD25+_rep2

description: gender: male


title: human non-Hodgkins lymphoma cell line, OCI-Ly19_rep1


title: human non-Hodgkins lymphoma cell line, NU-DUL-1_rep2


title: Treg_freshly sorted_CD4+CD25+_rep3

description: gender: male


title: human non-Hodgkins lymphoma cell line, NU-DUL-1_rep1


title: human non-Hodgkins lymphoma cell line, KARPAS-1106P_rep2


title: Tconv_freshly sorted_CD4+CD25-_rep3

description: gender: male

source_name: freshly sorted Tconv cells

tag: Tconv freshly sorted CD4+CD25-


title: Tconv_freshly sorted_CD4+CD25-_rep2

description: gender: male


title: human non-Hodgkins lymphoma cell line, NU-DHL-1_rep4


title: human non-Hodgkins lymphoma cell line, MHH-PREB-1_rep1


title: Tconv_freshly sorted_CD4+CD25-_rep1

description: gender: male


title: human non-Hodgkins lymphoma cell line, Jeko1


title: human non-Hodgkins lymphoma cell line, NU-DHL-1_rep3


title: Treg_culture_CD4+CD25+CD45RA+_rep3

description: gender: male

source_name: Treg expansion culture

tag: Treg culture CD4+CD25+CD45RA+


title: Treg_culture_CD4+CD25-RA-_rep3

description: gender: male

tag: Treg culture CD4+CD25-RA-


title: human non-Hodgkins lymphoma cell line, MHH-PREB-1_rep2


title: human non-Hodgkins lymphoma cell line, Farage

description: Farage

value: Farage


title: human non-Hodgkins lymphoma cell line, DoHH2


title: Treg_culture_CD4+CD25-RA-_rep4

description: gender: male


title: human non-Hodgkins lymphoma cell line, GRANTA-519


title: human non-Hodgkins lymphoma cell line, MC116


title: human non-Hodgkins lymphoma cell line, KARPAS-1106P_rep1


title: human non-Hodgkins lymphoma cell line, HT

description: HT

value: HT


title: Treg_culture_CD4+CD25+CD45RA+_rep4

description: gender: male


title: Treg_culture_CD4+CD25+CD45RA+_rep2

description: gender: male


title: human non-Hodgkins lymphoma cell line, FarageX1_rep2


title: human non-Hodgkins lymphoma cell line, FarageX1_rep1


title: human non-Hodgkins lymphoma cell line, DB

description: DB

value: DB


title: human non-Hodgkins lymphoma cell line, Karpas-422


title: human non-Hodgkins lymphoma cell line, CI-1_rep1


title: Treg_culture_CD4+CD25-RA-_rep2

description: gender: male


title: Treg_culture_CD4+CD25+CD45RA+_rep1

description: gender: male


title: human non-Hodgkins lymphoma cell line, CI-1_rep2


title: human non-Hodgkins lymphoma cell line, BJAB

description: BJAB

value: BJAB


title: human non-Hodgkins lymphoma cell line, A4_Fukada_rep2

value: human non-Hodgkins lymphoma


title: human non-Hodgkins lymphoma cell line, A3_Kawakami_rep1


title: Treg_culture_CD4+CD25-RA-_rep1

description: gender: male


title: 13483889 - pBIN18h vs pBINT0

status: Public on May 10 2009

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

country: France

institute: INRA

description: Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties.

hyb_protocol: pBINT0 Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - Media : soil hygrometry : 70% Temperature : 20°C Light : 12/12h

treatment_protocol: Name:Paraquat - time course study - abiotic stress,paraquat:. Paraquat (10 (u)M) was infiltrated in leaves with needleless syringe. each genotype at 0 (T0), 4 (T1) and 18 (T2) hours after Paraquat infiltration.

tag: cultivar

value: Columbia

tag: dev stage (boyes et al. plant cell 2001)

value: boyes 5.10


title: 13366282 - Ovex4h vs pBIN4h

hyb_protocol: pBIN4h Cy5 / Ovex4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13483890 - pBINT0 vs pBIN18h

hyb_protocol: pBIN18h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13483895 - Ovex18h vs pBIN18h

hyb_protocol: pBIN18h Cy5 / Ovex18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366277 - pBIN4h vs Asense4h

hyb_protocol: Asense4h Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

value: mutant (asense:silenced for expression of PLP2, a patatin-like LAH (At2g26560))

tag: dev stage(boyes et al. plant cell 2001)


title: 13483877 - Asense18h vs pBIN18h

hyb_protocol: pBIN18h Cy5 / Asense18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype mutant (asense

value: silenced for expression of PLP2, a patatin-like LAH (At2g26560))


title: Mesencephalon primary culture MesPC_rep3

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: To minimize biological variability four pregnant rats were sacrificed and the E11 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled (MesE11) or dissociated and the cells were cultured in duplicate. After 9 days in vitro the cultures were collected (MesPC). Three microarrays were hybridized with MesE11 and three with MesPC independent samples.

hyb_protocol: Affyemtrix standard protocol

scan_protocol: Affyemtrix standard protocol

data_processing: RMA

organism: Rattus norvegicus

source_name: rattus norvegicus mesencephalon primary cultures

label_protocol: Affyemtrix standard protocol

extract_protocol: Tri-Reagent isolation system (Sigma)

tag: tissue

value: mesencephalon

tag: sample type

value: primary culture

tag: days in vitro


title: human non-Hodgkins lymphoma cell line, A3_Kawakami_rep2


title: 13366279 - pBIN4h vs Ovex4h

hyb_protocol: Ovex4h Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13483894 - pBIN18h vs Ovex18h

hyb_protocol: Ovex18h Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366276 - pBIN4h vs pBINT0

hyb_protocol: pBINT0 Cy5 / pBIN4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia dev.stage (boyes et al. plant cell 2001):boyes 5.10


title: 13301348 - pBIN48h vs Ovex48h

hyb_protocol: Ovex48h Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - Media : soil Hygrometry : 70% Temperature : 20°C Light : 12/12h

treatment_protocol: Name:Botrytis cinerea infection - time course study - pathogen infection,botrytis cinerea:time 0hour .

tag: age

value: 7 week


title: 13301347 - Asense48h vs pBIN48h

hyb_protocol: pBIN48h Cy5 / Asense48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia mutant (asense:silenced for expression of PLP2, a patatin-like LAH (At2g26560))


title: 13500961 - pBIN18h vs Asense18h

hyb_protocol: Asense18h Cy5 / pBIN18h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13301349 - Ovex48h vs pBIN48h

hyb_protocol: pBIN48h Cy5 / Ovex48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mesencephalon primary culture MesPC_rep5


title: 13366278 - Asense4h vs pBIN4h

hyb_protocol: pBIN4h Cy5 / Asense4h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mesencephalon primary culture MesPC_rep4


title: Mesencephalon primary culture MesPC_rep6


title: 13301350 - pBINT0 vs OvexT0

hyb_protocol: OvexT0 Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366275 - pBINT0 vs pBIN4h

hyb_protocol: pBIN4h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13301352 - pBIN48h vs Asense48h

hyb_protocol: Asense48h Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mesencephalon primary culture MesPC_rep2


title: 13301351 - OvexT0 vs pBINT0

hyb_protocol: pBINT0 Cy5 / OvexT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mesencephalon at E11 MesE11_rep3

description: To minimize biological variability four pregnant rats were sacrificed and the E11 embryos were mixed obtaining three groups. Each group was treated separately. The ventral midbrains dissected from each group were pooled (MesE11) or dissociated and the cells were cultured in duplicate.

source_name: rattus norvegicus mesencephalon E11


title: 13300953 - pBINT0 vs pBIN48h

hyb_protocol: pBIN48h Cy5 / pBINT0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300954 - pBIN48h vs pBINT0

hyb_protocol: pBINT0 Cy5 / pBIN48h Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mesencephalon primary culture MesPC_rep1


title: Mesencephalon at E11 MesE11_rep2


title: Mesencephalon at E11 MesE11_rep1


title: ccRCC tumor and normal blood DNA pair 69

status: Public on May 09 2009

city: Houston

first: Xifeng

last: Wu

state: TX

address: 1155 pressler blvd.

department: Epidemiology

institute: UT M.D Anderson Cancer Center

description: Genomic DNA from ccRCC tumor and reference DNA from blood sample of the corresponding ccRCC patient were genotyped using Infinium HumanHap300 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from ccRCC tumor and normal blood DNA pairs was genotyped using Infinium HumanHap300 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

source_name: ccRCC tumor and blood

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using QIAamp DNeasy Blood and Tissue kit (QIAGEN, Valencia, CA).

tag: gender

value: female

value: ccRCC tumor and blood

tag: disease state

value: carcinoma


title: ccRCC tumor and normal blood DNA pair 78

value: male


title: ccRCC tumor and normal blood DNA pair 52


title: ccRCC tumor and normal blood DNA pair 67


title: ccRCC tumor and normal blood DNA pair 77


title: ccRCC tumor and normal blood DNA pair 56


title: ccRCC tumor and normal blood DNA pair 62


title: ccRCC tumor and normal blood DNA pair 57


title: ccRCC tumor and normal blood DNA pair 68


title: ccRCC tumor and normal blood DNA pair 74


title: ccRCC tumor and normal blood DNA pair 75


title: ccRCC tumor and normal blood DNA pair 63


title: ccRCC tumor and normal blood DNA pair 71


title: ccRCC tumor and normal blood DNA pair 65


title: ccRCC tumor and normal blood DNA pair 55


title: ccRCC tumor and normal blood DNA pair 60


title: ccRCC tumor and normal blood DNA pair 59


title: ccRCC tumor and normal blood DNA pair 53


title: ccRCC tumor and normal blood DNA pair 58


title: ccRCC tumor and normal blood DNA pair 76


title: ccRCC tumor and normal blood DNA pair 66


title: ccRCC tumor and normal blood DNA pair 64


title: ccRCC tumor and normal blood DNA pair 70


title: ccRCC tumor and normal blood DNA pair 73


title: ccRCC tumor and normal blood DNA pair 54


title: ccRCC tumor and normal blood DNA pair 61


title: ccRCC tumor and normal blood DNA pair 50


title: ccRCC tumor and normal blood DNA pair 72


title: ccRCC tumor and normal blood DNA pair 51


title: ccRCC tumor and normal blood DNA pair 49


title: ccRCC tumor and normal blood DNA pair 47


title: ccRCC tumor and normal blood DNA pair 48


title: ccRCC tumor and normal blood DNA pair 46


title: ccRCC tumor and normal blood DNA pair 39


title: ccRCC tumor and normal blood DNA pair 30


title: ccRCC tumor and normal blood DNA pair 43


title: ccRCC tumor and normal blood DNA pair 25


title: ccRCC tumor and normal blood DNA pair 45


title: ccRCC tumor and normal blood DNA pair 38


title: ccRCC tumor and normal blood DNA pair 32


title: ccRCC tumor and normal blood DNA pair 42


title: ccRCC tumor and normal blood DNA pair 26


title: ccRCC tumor and normal blood DNA pair 41


title: ccRCC tumor and normal blood DNA pair 23


title: ccRCC tumor and normal blood DNA pair 44


title: ccRCC tumor and normal blood DNA pair 24


title: ccRCC tumor and normal blood DNA pair 31


title: ccRCC tumor and normal blood DNA pair 33


title: ccRCC tumor and normal blood DNA pair 28


title: ccRCC tumor and normal blood DNA pair 29


title: ccRCC tumor and normal blood DNA pair 37


title: ccRCC tumor and normal blood DNA pair 36


title: ccRCC tumor and normal blood DNA pair 27


title: ccRCC tumor and normal blood DNA pair 22


title: ccRCC tumor and normal blood DNA pair 21


title: ccRCC tumor and normal blood DNA pair 35


title: ccRCC tumor and normal blood DNA pair 34


title: ccRCC tumor and normal blood DNA pair 40


title: Pool 4 Acute stage

city: Perth

first: Kathy

middle: Laura

last: McKenna

state: Western Australia

address: 100 Roberts Rd

country: Australia

institute: Institute for Child Health Research

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C on Affymetrix U133Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Microarray data were analysed in the open-source statistical software R employing the probe-level model (PLM) algorithm for background subtraction, normalization and summarization of probe set intensities.

label: Biotin

source_name: Acute samples

label_protocol: Labeled cRNA were prepared according to the standard Affymetrix protocol from 1 ug of total pooled RNA.

extract_protocol: Total RNA was extracted from cryopreserved PBMCs using TRIzol followed by RNeasy as according to the manufacturer's instructions. Equal amounts of RNA from 5 subjects were pooled, either at acute exacerbation or convalescent stage, to give a total of 10 pools for analysis.

treatment_protocol: Peripheral blood was collected during acute exacerbation post glucocorticoid treatment (inhaled salbutamol and ipratropium bromide at 20 min intervals for first hour, and oral prednisolone 1mg/kg) and at convalescence ≥ six weeks later and cryopreserved.

value: PBMC

value: Acute


title: Pool 5 Convalescent stage

source_name: Convalescence samples

value: Convalescence


title: Pool 3 Acute stage


title: Pool 5 Acute stage


title: Pool 3 Convalescent stage


title: Pool 2 Acute stage


title: Pool 1 Acute stage


title: Pool 2 Convalescent stage


title: Pool 4 Convalescent stage


title: ccRCC tumor and normal blood DNA pair 17


title: ccRCC tumor and normal blood DNA pair 20


title: ccRCC tumor and normal blood DNA pair 19


title: ccRCC tumor and normal blood DNA pair 18


title: Pool 1 Convalescent stage


title: ccRCC tumor and normal blood DNA pair 16


title: ccRCC tumor and normal blood DNA pair 14


title: ccRCC tumor and normal blood DNA pair 13


title: ccRCC tumor and normal blood DNA pair 9


title: ccRCC tumor and normal blood DNA pair  5


title: ccRCC tumor and normal blood DNA pair 15


title: ccRCC tumor and normal blood DNA pair 10


title: ccRCC tumor and normal blood DNA pair 8


title: ccRCC tumor and normal blood DNA pair  4


title: ccRCC tumor and normal blood DNA pair  7


title: ccRCC tumor and normal blood DNA pair  1


title: ccRCC tumor and normal blood DNA pair 11


title: ccRCC tumor and normal blood DNA pair  6


title: ccRCC tumor and normal blood DNA pair 12


title: ccRCC tumor and normal blood DNA pair 3


title: Slide 6: S. pyogenes wild type vs. CvfA- mutant

status: Public on May 08 2009

city: Carbondale

first: KyuHong

last: Cho

state: IL

address: 1125 Lincoln Dr. Room 131

department: Microbiology

institute: Southern Illinois University Carbondale

description: Wild type strain versus CvfA- mutant strain in stationary phase of growth

hyb_protocol: The tagged cDNAs from the appropriate samples were mixed and then allowed to hybridize with the array using a commercial buffer (MWG) at 42°C overnight. Following washing using 2× SSC, 0.2% SDS, at 65°C to remove unhybridized cDNAs, the detection reagents (Cyanine 3 and Cyanine 5 3DNA dendrimers, Genisphere) were added with incubation at 65°C for 3 h. Unbound detection reagents were removed by washing.

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence.

data_processing: What is submitted is the raw output of Scanarray. VALUE = log2 (test/ref)

organism: Streptococcus pyogenes

source_name: Streptocococcus pyogenes, CvfA- mutant, stationary phase of growth

label_protocol: Synthesis and labelling of cDNA used a commercial kit (3DNA Array 900, Genisphere).

growth_protocol: Overnight growth in C medium was diluted 1:20 in fresh C medium followed by incubation at 37°C to stationary phase of growth (8 hrs post-inoculation)

extract_protocol: Total RNA was isolated using glass beads (Lysing Matrix A, Q/BioGene) and a high-speed reciprocating shaking device (FP-120, Savant Instruments). RNA was further purified (RNeasy Mini Kit for RNA clean up, Qiagen) and contaminating DNA was removed by DNase. Total RNA concentration was calculated using absorbance at 260 nm. RNA was further analyzed by a fluorescent assay involving electrophoretic separation of RNA (Agilent 2100 Bioanalyzer), and rejected if the electropherogram (a diagram of fluorescence over time) showed degradation of RNA

tag: strain

value: CvfA- mutant

source_name: Streptocococcus pyogenes, wild type strain, stationary phase of growth

value: HSC5spc (Wild type)


title: ccRCC tumor and normal blood DNA pair  2


title: Slide 5: S. pyogenes wild type vs. CvfA- mutant


title: PR003

first: Federico

middle: A

last: Monzon

address: 6565 Fannin St., MS205

department: Pathology

institute: The Methodist Hospital Research Institute

description: ProstaticAdenocarcinoma_AndrogenInsensitive_FFPE_Rep3

hyb_protocol: Affymetrix Mapping 250K_Nsp Assay

scan_protocol: Affymetrix Mapping 250K Nsp Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0

label: Biotinilated - Fragmented PCR products

source_name: Prostatic Adenocarcinoma, DNA from Paraffin Embedded Tissue

label_protocol: Standard labeling protocol for FFPE tissue based on Affymetrix Mapping 250K Nsp Assay. Startup DNA amount is 1ug

extract_protocol: Deparaffinization followed by Qiagen DNeasy Blood and Tissue kit by manufacturer's instructions

tag: Sex:	M


title: PR004

description: ProstaticAdenocarcinoma_AndrogenInsensitive_FFPE_Rep4


title: PR002

description: ProstaticAdenocarcinoma_AndrogenInsensitive_FFPE_Rep2


title: Slide 3: S. pyogenes wild type vs. CvfA- mutant

source_name: Streptocococcus pyogenes,CvfA- mutant, stationary phase of growth


title: Slide 4: S. pyogenes wild type vs. CvfA- mutant


title: placenta 106

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: placenta

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

organism: Mus musculus

source_name: placenta

label_protocol: 2 ug total RNA was used with the GeneChip WT Sense Target Labeling Kit

extract_protocol: Total RNA was isolated from cell pellets using Trizol (Invitrogen, Carlsbad, CA) followed by clean up using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: RNA extraction from tissues of naïve male (except females for specific organs) C57BL/6J mice, 8-10 weeks of age

value: placenta


title: hippocampus 100

description: hippocampus

source_name: hippocampus

value: hippocampus


title: Slide 2: S. pyogenes wild type vs. CvfA- mutant


title: umbilical cord 101

value: umbilical cord


title: umbilical cord 102


title: mammary gland lactating 104

value: mammary gland  lact


title: placenta 105

description: placenta


title: Slide 1: S. pyogenes wild type vs. CvfA- mutant


title: hippocampus 99

description: hippocampus


title: mammary gland lactating 103


title: PR005

description: ProstaticAdenocarcinoma_AndrogenInsensitive_FFPE_Rep5


title: ccRCC tumor and normal blood DNA pair 79


title: ccRCC tumor and normal blood DNA pair 80


title: bone 97

description: bone

source_name: bone

value: bone


title: adipose white 94

value: adipose white


title: bone 98

description: bone


title: adipose white 93


title: adrenal gland 95

value: adrenal gland


title: adrenal gland 96


title: amygdala 92

description: amygdala

source_name: amygdala

value: amygdala


title: amygdala 91

description: amygdala


title: epidermis 90

description: epidermis

source_name: epidermis

value: epidermis


title: lung 88

description: lung

source_name: lung

value: lung


title: epidermis 89

description: epidermis


title: liver 86

description: liver

source_name: liver

value: liver


title: lung 87

description: lung


title: uterus 84

description: uterus

source_name: uterus

value: uterus


title: bone marrow 77

value: bone marrow


title: pancreas 81

description: pancreas

source_name: pancreas

value: pancreas


title: Adenovirus vector treated animal #1 vs mock treated: 1 hour post-treatment

status: Public on May 13 2009

city: Richmond

first: Paul

last: Fawcett

state: VA

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41858.gif

hyb_protocol: not provided

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Mock treated animal liver: 1 hour post-treatment

label_protocol: not provided

extract_protocol: not provided

tag: treatment

value: mock treated - 1 hour post-treatment

source_name: Adenovirus vector treated animal liver: 1 hour post-treatment

value: adenovirus vector treated - 1 hour post-treatment


title: C3H/10T1/2 75

tag: cell line


title: liver 85

description: liver


title: spinal cord 80

value: spinal cord


title: uterus 83

description: uterus


title: C3H/10T1/2 76


title: RAW 264 7 73


title: nih 3T3 72

value: nih 3T3


title: spinal cord 79


title: C2C12 64


title: mIMCD-3 68


title: RAW 264 7 74


title: pancreas 82

description: pancreas


title: bone marrow 78


title: neuro2a 70


title: Baf3 62


title: nih 3T3 71


title: 3T3-L1 60


title: min6 66


title: C2C12 63


title: mIMCD-3 67


title: Baf3 61


title: macrophage bone marrow 6hr LPS 55

tag: cell type

value: macrophage bone marrow 6hr LPS


title: macrophage bone marrow 6hr LPS 56


title: neuro2a 69


title: macrophage bone marrow 24hr hr LPS 58

value: macrophage bone marrow 24hr hr LPS


title: 3T3-L1 59


title: macrophage bone marrow 2hr LPS 53

value: macrophage bone marrow 2hr LPS


title: min6 65


title: embryonic stem cell line V26 2 p16 50

value: embryonic stem cell line V26 2 p16


title: macrophage bone marrow 0hr 52

value: macrophage bone marrow 0hr


title: embryonic stem cell line V26 2 p16 49


title: macrophage bone marrow 0hr 51


title: macrophage bone marrow 2hr LPS 54


title: testis 37

description: testis

source_name: testis

value: testis


title: embryonic stem cell line Bruce4 p13 47

value: embryonic stem cell line Bruce4 p13


title: macrophage peritoneal LPS thioglycollate 7hrs 45

description: macrophage_peritoneal_LPS_thioglycollate_7hrs


title: macrophage peritoneal LPS thioglycollate 7hrs 46


title: Paracoccidioides brasiliensis_yeasts_14 days in culture_flask2_rep1

type: mixed

city: San Jose

first: Jomar

middle: Patrício

last: Monteiro

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description:
Cited Bibliography:
Clemons, K. V., Feldman, D. & Stevens, D. A. (1989). Influence of oestradiol on protein expression and methionine utilization during morphogenesis of Paracoccidioides brasiliensis. J Gen Microbiol 135, 1607-1617.
Gadgil, M., Lian, W., Gadgil, C., Kapur, V. & Hu, W. S. (2005). An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays. BMC Genomics 6, 66.
Li, X., Gu, W., Mohan, S. & Baylink, D. J. (2002). DNA microarrays: their use and misuse. Microcirculation 9, 13-22.
McCullough, M. J., DiSalvo, A. F., Clemons, K. V., Park, P. & Stevens, D. A. (2000). Molecular epidemiology of Blastomyces dermatitidis. Clin Infect Dis 30, 328-335.
Oefner, P. J., Hunicke-Smith, S. P., Chiang, L., Dietrich, F., Mulligan, J. & Davis, R. W. (1996). Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res 24, 3879-3886.
Restrepo, A. & Jimenez, B. E. (1980). Growth of Paracoccidioides brasiliensis yeast phase in a chemically defined culture medium. J Clin Microbiol 12, 279-281.
Stover, E. P., Schar, G., Clemons, K. V., Stevens, D. A. & Feldman, D. (1986). Estradiol-binding proteins from mycelial and yeast-form cultures of Paracoccidioides brasiliensis. Infect Immun 51, 199-203.
Talaat, A. M., Howard, S. T., Hale, W. t., Lyons, R., Garner, H. & Johnston, S. A. (2002). Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 30, e104.
Thorstenson, Y. R., Hunicke-Smith, S. P., Oefner, P. J. & Davis, R. W. (1998). An automated hydrodynamic process for controlled, unbiased DNA shearing. Genome Res 8, 848-855.
Williams, B. A., Gwirtz, R. M. & Wold, B. J. (2006). Genomic DNA as a general cohybridization standard for ratiometric microarrays. Methods Enzymol 410, 237-279.

hyb_protocol: PREHYBRIDIZATION Microarray slides were prepared for hybridization as follows: spotted DNA was cross-linked to the slide under a UV light source (150-300 mjoules on a UV Stratalinker® 1800; Stratagene).  Slides were incubated in 500 ml prehybridization solution (3x SSC containing 0.1 % SDS and 0.1 mg/ml bovine serum albumin (Sigma-Aldrich)) for 90 minutes at 50 C in a water bath (Li et al., 2002).  Slides were washed sequentially with water at ~100 C for 1-2 minutes, water for at room temperature 1-2 minutes and dipped five times in ethanol.  The slides were placed in 50 ml polypropylene centrifuge tubes (Corning) and centrifuged for 5 minutes at 500 x g or until dry.  Slides were stored in clean, tightly sealed containers. HYBRIDIZATION Samples of labeled nucleic acids for hybridization were concentrated using a Microcon® YM-30 Centrifugal Filter Device (Millipore) and suspended to 40 μl with 3X saline-sodium citrate buffer (Sigma-Aldrich, St. Louis, MO), 0.1% sodium dodecyl sulfate (Sigma-Aldrich). These samples were incubated at 100oC for 2 minutes, 37 C for 15-25 minutes, transferred onto a microarray slide and covered with a coverslip and placed in hybridization chambers (see supplemental material for details).  Hybridization was carried at 50 C for 14 to 18 hours followed by washing the slides with 2X SSC with 0.03% SDS, 2X SSC, 1X SSC and 0.2X SSC for 2-5 minutes in each solution (500 ml volume/solution) and spin drying. Slides were scanned within 24 hours (GenePix® 4000B Microarray Scanner, Axon Instruments, Union City, CA).  All hybridization experiments were done in duplicate from each of two independent cultures.

scan_protocol: Hybridized microarrays were scanned in a GenePix® 4000B Microarray Scanner (Axon Instruments, Union City, CA). Raw data were extracted by GenePix® Pro 6.0 Microarray Image Analysis software (Axon) and analyzed using Array-A-Lizer (Petri et al., 2004) for slide quality control estimations (background intensity and spot intensity distribution).  Scanner photomultiplier tube gains for both detection channels, 635 nm (Cy5-red color) and 532 nm (Cy3-green color), were 540 and 500, respectively.

data_processing: Gene expression data underwent global normalization using the R statistical package to perform quantile normalization of the global reference channel by computing the centroid of all global reference signatures, and performing a loess fit of each individual global reference signature to the centroid.  The loess curve for a given sample was then used to scale both channels for each gene in that sample.  Data was further normalized in GeneSpring GX 7.3.1 (Agilent Technologies, Palo Alto, CA) as follows: per spot to the gDNA channel, and per gene to each gene’s respective median (Talaat et al., 2002).  For M versus Y gene expression, per slide normalization consisted of selecting a list of spots where gDNA intensities showed a linear relationship with cDNA intensities in M versus A plots (M = log2(Cy5/Cy3) versus A = log2(Cy5xCy3)1/2) across all time points in both M and Y, as well as being below a two-fold change in gene expression values.  One hundred and two spots satisfied these criteria and were used as positive controls for per slide normalization process.

organism: Paracoccidioides brasiliensis

source_name: P. brasiliensis yeast form, 14 days in culture

label_protocol: In brief, 100 μg of total RNA, in a volume of ≤ 10 μl, was used with the addition of 4 μg of Oligo-dT primer (5’ TTT TTT TTT TTT TTT TTT TTV N 3’) and nuclease-free water to a final volume of 15.4 μl.  This mixture was incubated at 70 C for 10 minutes and cooled on ice.  While on ice, 6 μl of 5X First Strand Buffer (Invitrogen), 3 μl 0.1 M DTT (dithiothreitol), 0.6 μl of dNTPs (25 mM dGTP, dATP, dCTP and 10 mM dTTP, Promega), 3 μl of Cy5-dUTP (Amersham Biosciences, Piscataway, NJ), and 400 U SuperScriptTM II Reverse Transcriptase (200 U/μl; Invitrogen) were added.  This mixture was incubated at 42 C for 1.5 h.  Reverse transcriptase activity was boosted by adding an additional 100 U of reverse transcriptase and incubation at 42 C for another 30 minutes.  RNA was degraded with 15 μl of 0.1 N NaOH and incubation at 70 C for 30 minutes.  NaOH was neutralized by the addition of 15 μl 0.1 N HCl and samples were maintained on ice prior to use.

growth_protocol:
Yeast (Y) cultures were maintained on modified McVeigh/Morton (MVM) agar slants (Restrepo & Jimenez, 1980) at 36 C and were transferred every 10-15 days.  Mycelial (M) cultures were maintained on MVM slants at ambient temperature and were transferred monthly.
Spent culture filtrate was used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as previously described (Clemons et al., 1989; Stover et al., 1986) for the growth of liquid cultures M and Y prior to DNA and RNA extractions.
For total RNA extractions, one Y or two M five-day-old slants were used to inoculate 150 ml of supplemented liquid MVM media and incubated on a gyratory shaker at 150 rpm, at 36 C for Y or at ambient temperature for M, for 5, 8 or 14 days.  Liquid cultures were evaluated for contaminating organisms by microscopy and by plating samples on 5% sheep blood agar followed by incubation for 2-3 days at 36 C.

extract_protocol:
Cell disruption for total RNA extraction was performed as follows: fungal cells were collected by centrifugation (5 minutes at 500 x g), snap-frozen in liquid nitrogen, and 1 ml of TRIzol (Invitrogen Life Technologies, Carlsbad, CA) added per 1 g of pelleted cells.  After thawing, cells were mechanically disrupted with 0.5 mm zirconia/silica beads (Biospec) using a BeadBeater.  These homogenates were used in the extraction protocol provided by TRIzol’s manufacturer.
Removal of DNA copurified with total RNA was done in reactions containing 10 μg total RNA, 10 μl RQ1 DNase 10X reaction buffer, 10 units RQ1 RNase-free DNase, 40 units RNasin® Plus RNase Inhibitor (all from Promega, Madison, WI) and nuclease-free water (Sigma-Aldrich, St. Louis, MO) added to a final reaction volume of 100 μl.  Reactions were incubated at 37 C for one hour followed by incubation at 70 C for 30 minutes to inactivate the DNase.
The quantity and quality of the extracted RNA were assessed by A260nm/A280nm ratio and electrophoresis through a 1.5% agarose gel stained with ethidium bromide (presence of intact 18S and 28S ribosomal RNA bands) and visualized by UV transillumination at 302 nm.  Contaminating gDNA was removed using RNase-free DNase (RQ1 RNase-free DNase, Promega, Madison, WI) per the manufacturer’s instructions.

treatment_protocol: Snap frozen in liquid nitrogen for brief storage in -80 C prior to total RNA extraction.

tag: channel type

value: sample

tag: isolate

value: pb01 (atcc:MYA-826)

tag: morphologic form

value: yeast

tag: growth

value: modified McVeigh/Morton liquid media for 14 days

source_name: P. brasiliensis yeast, sheared genomic DNA

label_protocol: Cy3- or Cy5-labeled P. brasiliensis gDNA was synthesized from 250 ng of sheared gDNA using the BioPrime® Array CGH Genomic Labeling System (Invitrogen) following the manufacturer’s instructions.  Cy3-labeled gDNA was used as a control to facilitate comparisons between slides and data integration in future experiments (Gadgil et al., 2005; Talaat et al., 2002; Williams et al., 2006).  Cy5-labeled gDNA was used in self-to-self hybridizations along with Cy3-labeled gDNA during microarray validation procedures.

growth_protocol:
Yeast (Y) cultures were maintained on modified McVeigh/Morton (MVM) agar slants (Restrepo & Jimenez, 1980) at 36 C and were transferred every 10-15 days.  Mycelial (M) cultures were maintained on MVM slants at ambient temperature and were transferred monthly.
Spent culture filtrate was used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as previously described (Clemons et al., 1989; Stover et al., 1986) for the growth of liquid cultures M and Y prior to DNA and RNA extractions.
For genomic DNA extractions, two five-day-old Y slants were used to inoculate 150 ml of supplemented liquid MVM media and incubated on a gyratory shaker at 150 rpm, at 36 C for 4 days.  Liquid cultures were evaluated for contaminating organisms by microscopy and by plating samples on 5% sheep blood agar followed by incubation for 2-3 days at 36 C.

extract_protocol:
Genomic DNA (gDNA) was extracted from Y collected from four-day-old liquid cultures (36 C, shaking at 150 rpm) using previously described methodology (McCullough et al., 2000).
Modifications to the original DNA extraction protocol included reduction of cell disruption time to 15 seconds at the high speed setting on a BeadBeater apparatus (Biospec Products, Inc., Bartlesville, OK) and precipitation of DNA using 100% ethanol (Gold Shield Chemical Co., Hayward, CA) following the RNase digestion step.
The quantity and quality of the extracted DNA were assessed using a spectrophotometric absorbance ratio (A260nm/A280nm) and by electrophoresis through a 0.8% agarose gel stained with ethidium bromide and visualized by ultraviolet (UV) transillumination.
Genomic DNA was sheared hydrodynamically into ~1.5 Kb fragments using a HydroShear® apparatus (Genomic Solutions, Ann Arbor, MI) as previously described (Oefner et al., 1996; Thorstenson et al., 1998).  Adequacy of DNA shearing was assessed by 1.5% agarose gel electrophoresis and visualized by UV after ethidium bromide staining.

treatment_protocol: None.

value: reference

value: modified McVeigh/Morton liquid media for 4 days


title: embryonic stem cell line Bruce4 p13 48


title: mammary gland non-lactating 40

value: mammary gland non-lactating


title: macrophage peritoneal LPS thioglycollate 1hrs 43

description: macrophage_peritoneal_LPS_thioglycollate_1hrs


title: macrophage peritoneal LPS thioglycollate 0hrs 41

description: macrophage_peritoneal_LPS_thioglycollate_0hrs


title: macrophage peritoneal LPS thioglycollate 0hrs 42


title: macrophage peritoneal LPS thioglycollate 1hrs 44


title: mammary gland non-lactating 39


title: pituitary 36

description: pituitary

source_name: pituitary

value: pituitary


title: Paracoccidioides brasiliensis_yeasts_14 days in culture_flask1_rep1


title: Paracoccidioides brasiliensis_yeasts_14 days in culture_flask2_rep2


title: pituitary 35

description: pituitary


title: testis 38

description: testis


title: dorsal root ganglia 33

value: dorsal root ganglia


title: Paracoccidioides brasiliensis_yeasts_14 days in culture_flask1_rep2


title: Paracoccidioides brasiliensis_yeasts_8 days in culture_flask2_rep1

source_name: P. brasiliensis yeast form, 8 days in culture

value: modified McVeigh/Morton liquid media for 8 days


title: Paracoccidioides brasiliensis_yeasts_8 days in culture_flask1_rep1


title: Paracoccidioides brasiliensis_yeasts_8 days in culture_flask2_rep2


title: mouse 4 with the human c-Src transgene inserted downstream of the mouse metallothionein promoter

city: Hershey

first: Rosalyn

middle: B.

last: Irby

state: PA

address: 500 University Drive

department: Medicine

institute: Pennsylvania State University Hershey Medical Center

description: liver tissue from 14 month old C57Bl/6 mouse

hyb_protocol: Array hybridized at 37C for 18h

scan_protocol: Array scanned with Axon GenePixPro 4000B

data_processing: The output was generated for GeneSpring import by CodeLink Expression Analysis Software v4.1 (GE Healthcare), which creates a txt file compatible with GeneSpring. Raw values represent the final number of the spot after background is subtracted out. Normalized values represent median global normialzation method - raw intensity/median intensity of all spots on the array

label: Alexa-647 Streptavidin

label_protocol: Biotin labeled cRNA was prepared by linear amplification of the poly(A)+ RNA population within the total RNA sample

extract_protocol: TRIzol reagent (Invitrogen) Cleanup with Qiagen Rneasy

tag: genotype

value: liver

value: 14 month old


title: Paracoccidioides brasiliensis_yeasts_5 days in culture_flask3_rep1

source_name: P. brasiliensis yeast form, 5 days in culture

value: modified McVeigh/Morton liquid media for 5 days


title: heart 27

description: heart

source_name: heart

value: heart


title: macrophage bone marrow 24hr hr LPS 57

value: macrophage bone marrow 24hr hr LPS


title: Paracoccidioides brasiliensis_yeasts_5 days in culture_flask3_rep2


title: wild type mouse liver control 4

value: wild type


title: dorsal root ganglia 34


title: olfactory bulb 32

value: olfactory bulb


title: mouse 1 with the human c-Src transgene inserted downstream of the mouse metallothionein promoter


title: Paracoccidioides brasiliensis_yeasts_5 days in culture_flask1_rep2

value: sample


title: wild type mouse liver control 2


title: mouse 3 with the human c-Src transgene inserted downstream of the mouse metallothionein promoter


title: Paracoccidioides brasiliensis_yeasts_8 days in culture_flask1_rep2

value: pb01 (atcc:MYA-826)


title: Paracoccidioides brasiliensis_yeasts_5 days in culture_flask1_rep1

value: yeast


title: Pooled lung tissue (n=8) 7 days after pneumonectomy

city: North Grafton

first: Julia

last: Paxson

state: MA

address: 200 Westboro Road

department: Clinical Sciences

institute: Tufts Cummings School of Veterinary Medicine

description: Gene expression data from 8 pooled lung tissue samples 7 days after left unilateral pneumonectomy

hyb_protocol: Chip hybridization was performed as described in the Affymetrix GeneChip Expression Analysis Technical Manual using Affymetrix Mouse Genome 430 2.0 GeneChips and the One-Cycle cDNA Synthesis and HT IVT Labeling kits (Affymetrix Inc.).

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner.

data_processing: The initial goal in the analysis was to identify genes regulated in the comparison between pneumonectomized and sham-operated animals. By treating all time points as replicates within their respective groups two datasets were created (PNY and SHAM), each with an n = 4. The corresponding Affymetrix CEL files were background corrected, summarized and quantile-normalized using the RMA library in BioConductor (http:www.bioconductor.org), yielding one expression value per probe set for each of the 8 arrays.  Based on the ‘Rank Products’ algorithm proposed by Brietling, et. al, the RankProd library was employed to find differentially expressed genes.  This algorithm works by performing comprehensive pair-wise comparisons to calculate a rank statistic RPg, the probability of seeing the observed, pair-wise expression patterns for any given gene g.  As a vehicle for measuring statistical significance a non-parametric P-value is also calculated, using 1000 permutations to determine how often the calculated RPg statistic would occur by chance alone. Finally, the RankProd library compares average expression between the two groups to derive a fold-change value. Genes with a reported P-value < 0.001 and a fold-change > 1.5 or < -1.5 were selected for further investigation.     In a second analysis, the focus was shifted to temporal changes in gene expression during lung regeneration as opposed to overall transcriptomic patterns. With only one array per experimental condition at each time point, derivation of statistical measures and the subsequent search for truly differentially expressed genes can be challenging. However, the S-Score algorithm described by Zhang et al. (2002) and Kerns et al. (2003) provides a method for determining statistical significance when biological replicates are not available by applying pairwise comparisons to probe-level data. On average, the Affymetrix 3’ IVT platform contains 22 probes for every transcript represented on the array. Using this information directly, the S-Score algorithm has shown an increased sensitivity when compared to many other existing analysis methods without sacrificing specificity, and can produce accurate results when no biological replicates are present (This is particularly applicable and appropriate to our individual time point datasets in which we have only one paired array set for each time point. Using the S-Score algorithm, the relative change in probe pair intensity is calculated to convert the probe pair signal differences into multiple measurements with equalized errors. The relative changes for each probe pair are then summed to form the S-score, which represents a single measure of the significance of change for the gene in question. By definition, S-score is related to P-value by an exponential relation, and a value of 3 corresponds to a P-value of 0.003 . Therefore, genes with an S-score > 3.0 or < - 3.0 (P < 0.003) were selected for further analysis.

source_name: Lung tissue, 7 days after left unilateral pneumonectomy

label_protocol: Labeling was performed as described in the Affymetrix GeneChip Expression Analysis Technical Manual using Affymetrix Mouse Genome 430 2.0 GeneChips and the One-Cycle cDNA Synthesis and HT IVT Labeling kits (Affymetrix Inc.).

growth_protocol: Mice used in this study were adult (10-12 week) female C57BL/6 (20-25g) obtained from Jackson Laboratories.

extract_protocol: The mice were anesthetized as above at 6 hours, 1 day, 3 days and 7 days after surgery (PNY or SHAM) then euthanized by cervical dislocation. The pulmonary vasculature was perfused with ice cold Hanks balanced salt solution, the trachea cannulated, and the lungs removed en bloc. RNA preservation was achieved by flooding the lung intratracheally with RNAlater solution (Qiagen #76104), followed by storage of lung tissue samples in RNAlater at -80ºC. Equal amounts of lung tissue were pooled from eight animals in each group (PNY or SHAM at each of 4 time points) to minimize biological variability. Total RNA was prepared from the dissected lung tissue using the Qiagen RNAeasy mini kit (Qiagen #74104) according to the manufacturer’s directions. The total RNA samples from the primary purification were purified a second time on Qiagen RNAeasy columns according to the manufacturer’s instructions. Total RNA concentrations, A260/A280 and A260/A230 ratios was determined using a NanoDrop ND1000 spectrophotometer.

treatment_protocol: Mice were anesthetized by intraperitoneal injection of ketamine (50-75 mg/kg) and xylazine (5 mg/kg), and then received 2ml of warmed normal saline and 100mg/kg sodium ampicillin subcutaneously. Orotracheal intubation was performed under direct visualization using a 20-gauge catheter (BD Insyte catheter; Becton, Dickinson and Co, Franklin Lakes NJ) over a flexible stylet. Mice were secured in supine position, and mechanically ventilated (AUT6110, Buxco Electronics, Wilmington, NC) at 200 tidal breaths of 0.3 ml of room air per minute, at positive end-expiratory pressure of 3 cm H2O during surgery and recovery. After achieving adequate anesthetic depth (absence of response to toe-pinch) the left thoracic wall was clipped and disinfected. The skin, chest wall and pleura were incised at the 5th intercostal space, and the left lung was gently lifted through a ~5-7mm incision and ligated at the hilum with 4-0 silk (Sofsilk, Synture Norwalk Ct). The lungs were then inflated to 30 cmH20 airway pressure, and the chest wall closed during this inflation with a single interrupted suture. The skin was closed with 5-0 PDS in a simple interrupted pattern. Mice were extubated at the onset of vigorous spontaneous breathing. The mice recovered from surgery in a warmed cage, and post-operative pain was managed with buprenorphine subcutaneously (0.05mg/kg) as soon as mice showed conscious motor control, and every 12 hours thereafter as needed (<3 days). Chow, nutrient gel (on the cage floor), and water were provided ad libitum. Sham pneumonectomy animals underwent an identical procedure, except that after the thoracotomy, the chest was left open for 5 minutes to simulate the conditions of the pneumonectomy group without removal of the left lung, then closed as described.

value: Female

value: 10-12 weeks

value: left unilateral pneumonectomy

tag: time

value: 7 days


title: wild type mouse liver control 1

tag: tissue


title: olfactory bulb 31


title: Paracoccidioides brasiliensis_mycelia_14 days in culture_flask2_rep2

source_name: P. brasiliensis mycelial form, 14 days in culture

value: mycelia

value: modified McVeigh/Morton liquid media for 14 days

value: modified McVeigh/Morton liquid media for 4 days

value: reference


title: Pooled lung tissue (n=8) 7 days after sham thoracotomy

description: Gene expression data from 8 pooled lung tissue samples 7 days after sham thoracotomy

source_name: Lung tissue, 7 days after sham thoracotomy

value: sham thoracotomy


title: stomach 24

description: stomach

source_name: stomach

value: stomach


title: Paracoccidioides brasiliensis_mycelia_14 days in culture_flask2_rep1


title: Paracoccidioides brasiliensis_mycelia_14 days in culture_flask1_rep2


title: adipose brown 30

value: adipose brown


title: intestine small 21

value: intestine small


title: Paracoccidioides brasiliensis_mycelia_14 days in culture_flask1_rep1


title: stomach 23

description: stomach


title: Pooled lung tissue (n=8) 3 days after sham thoracotomy

description: Gene expression data from 8 pooled lung tissue samples 3 days after sham thoracotomy

source_name: Lung tissue, 3 days after sham thoracotomy

value: 3 days


title: heart 28

description: heart

value: heart


title: Pooled lung tissue (n=8) 3 days after pneumonectomy

description: Gene expression data from 8 pooled lung tissue samples 3 days after left unilateral pneumonectomy

source_name: Lung tissue, 3 days after left unilateral pneumonectomy


title: intestine small 22


title: Paracoccidioides brasiliensis_mycelia_8 days in culture_flask2_rep2

source_name: P. brasiliensis mycelial form, 8 days in culture

value: sample

value: modified McVeigh/Morton liquid media for 8 days


title: hypothalamus 26

description: hypothalamus

source_name: hypothalamus

value: hypothalamus


title: Pooled lung tissue (n=8) 1 day after sham thoracotomy

description: Gene expression data from 8 pooled lung tissue samples 1 day after sham thoracotomy

source_name: Lung tissue, 1 day after sham thoracotomy

value: Female

value: 1 day


title: Paracoccidioides brasiliensis_mycelia_8 days in culture_flask2_rep1

value: pb01 (atcc:MYA-826)

value: yeast


title: spleen 20

description: spleen

source_name: spleen

value: spleen


title: Pooled lung tissue (n=8) 1 day after pneumonectomy

description: Gene expression data from 8 pooled lung tissue samples 1 day after left unilateral pneumonectomy

source_name: Lung tissue, 1 day after left unilateral pneumonectomy

value: 10-12 weeks

value: left unilateral pneumonectomy


title: prostate 17

description: prostate

source_name: prostate

value: prostate


title: Paracoccidioides brasiliensis_mycelia_8 days in culture_flask1_rep2

value: mycelia

source_name: P. brasiliensis yeast, sheared genomic DNA

value: reference

value: modified McVeigh/Morton liquid media for 4 days


title: prostate 16

description: prostate


title: hypothalamus 25

description: hypothalamus


title: F3-treated THP-1 cells for 24 hrs, biological rep2

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

description: established from the peripheral blood of a 1-year-old boy with acute monocytic leukemia (AML) at relapse in 1978; the cells can be used for induction of differentiation studies

hyb_protocol: see the Affymetrix website

scan_protocol: see the Affymetrix website

data_processing: Affymetrix Microarray Suite v5.0 software

source_name: human acute monocytic leukemia

label_protocol: see the Affymetrix website

growth_protocol: The human acute monocytic leukemia THP-1, and was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany)

extract_protocol: RNA Midi Kit from Qiagen

treatment_protocol: Cells were treated with F3 at a final concentration of 30 ug/mL for 6 or 24 hours. Controlled samples of un-induced cells were treated in the same way with the same amount of medium.


title: Paracoccidioides brasiliensis_mycelia_8 days in culture_flask1_rep1


title: Pooled lung tissue (n=8) 6 hours after sham thoracotomy

description: Gene expression data from 8 pooled lung tissue samples 6 hours after sham thoracotomy

source_name: Lung tissue, 6 hours after sham thoracotomy

value: sham thoracotomy

value: 6 hours


title: F3-treated THP-1 cells for 24 hrs, biological rep1


title: F3-treated THP-1 cells for 6 hrs, biological rep2


title: Paracoccidioides brasiliensis_mycelia_5 days in culture_flask2_rep1

source_name: P. brasiliensis mycelial form, 5 days in culture

value: modified McVeigh/Morton liquid media for 5 days


title: Paracoccidioides brasiliensis_mycelia_5 days in culture_flask2_rep2

value: sample


title: skeletal muscle 18

value: skeletal muscle


title: ovary 15

description: ovary

source_name: ovary

value: ovary


title: Colon epithelium, Stat3flfl VilCre+, biolrep2

city: Erlangen

first: Clemens

last: Neufert

address: Ulmenweg 18

department: First Department of Medicine

description: Gene expression data from  acute DSS colitis

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430 2.0 in Affymetrix GeneChip Hybridization oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Arrayassist version 5.5.1 (Stratagene) using GC-RMA as normalization method, followed by log scale transformation, grouping (cre- vs cre+), baseline transformation and advanced significance analysis including unpaired t-test.

source_name: colon epithelium, DSS colitis (2.5%), d5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were kept under SPF condition, Colitis was induced by dextran sodium sulphate (2.5 %) in the drinking water for 5 days

extract_protocol: Total RNA was purified by RNeasy Microkit as recommended by the manufacturer (Qiagen) including on column DNA digestion as recommended by the manufacturer (Qiagen)

value: Colon epithelium

value: Stat3floxflox VillinCre+


title: Pooled lung tissue (n=8) 6 hours after pneumonectomy

description: Gene expression data from 8 pooled lung tissue samples 6 hours after left unilateral pneumonectomy

source_name: Lung tissue, 6 hours after left unilateral pneumonectomy

value: Female